BIOL 3451 1st Edition Lecture 16 Outline of Last Lecture I. 12.3 Specialized Chromosomes Reveal Variations in the Organization of DNAII. 12.4 DNA Is Organized into Chromatin in EukaryotesIII. 12.5 Chromosome Banding Differentiates Regions along the Mitotic ChromosomeIV. 12.6 Eukaryotic Genomes Demonstrate Complex Sequence Organization Characterized by Repetitive DNAV. 12.7 The Vast Majority of a Eukaryotic Genome Does Not Encode Functional GenesVI. 13.1 The Genetic Code Uses Ribonulcleotide Bases as “Letters”VII. 13.2 Early Studies Established the Basic Operational Patterns of the CodeOutline of Current Lecture I. 13.2 Early Studies Established the Basic Operational Patterns of the CodeII. 13.3 Studies by Nirenberg, Matthaei, and Others Led to Deciphering of the CodeIII. 13.4 The Coding Dictionary Reveals Several Interesting Patterns among the 64 CodonsIV. 13.5 The Genetic Code Has Been Confirmed in Studies of Phage MS2V. 13.6 The Genetic Code Is Nearly UniversalVI. 13.7 Different Initiation Points Create Overlapping GenesVII. 13.8 Transcription Synthesizes RNA on a DNA TemplateVIII. 13.9 Studies with Bacteria and Phages Provided Evidence for the Existence of mRNAIX. 13.10 RNA Polymerase Directs RNA SynthesisX. 13.11 Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several WaysCurrent LectureI. 13.2 Early Studies Established the Basic Operational Patterns of the Codeo Genetic code reads 3 nucleotides at a time continuously It is degenerate: some amino acids are specified by more than one codon Nonsense codon: causes protein to terminate; they just mean stopII. 13.3 Studies by Nirenberg, Matthaei, and Others Led to Deciphering of the Codeo In vitro protein synthesizing system and produce synthetic mRNA using: Polynucleotide phosphorylase: breaks phosphodiester bond;- How we discovered genetic code(Figure 13.3) Made homopolymers (RNA nucleotides with only one type of ribonucleotide) to the in vitro translation systemThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- Helped decipher which amino acids were encoded by the first few codonsbased on which amino acids were incorporated into the polypeptide (Table 13.1) RNA Heteropolymers (two or more different ribonucleosides) - Used to decipher more codons doing same method(Figure 13.4)o Triplet Binding assay (Nirenberg and Leder): determines other specific codon assignments Ribosomes bind to single codon (3 nucleotides) and complementary amino acid-charged tRNA will bind to it Fig. 13.5, Table 13.2o Long RNAs with di-, tri-, an tetranucleotide repeats were used for in vitro translation to determine more codon assignments Figure 13.6 and Table 13.3III. 13.4 The Coding Dictionary Reveals Several Interesting Patterns among the 64 Codonso Genetic code is degenerate, with many amino acids specified by more than one codono Only tryptophan and methionine are encoded by single codon o (Fig 13.7): UCAG table; developed by Crick Look at how the table is organized: when have mutation in last nucleotide, not much difference in end outcome bc you get a very functionally similar amino acid Tryptophan: probably last amino acid added Methionine: first one for all proteinso Wobble hypothesis: predicts initial two ribonucleotides of triplet codes are often more critical than the third; in third position, doesn’t really matter and is less constrained spatially Table 13.4 (anticodon-codon base pairing rules)- A only U- C only G- G can pick up C or G- U can pick up A or G- I can pick up A, U or Co Genetic code shows order in that chemically similar amino acids often share one or two middle bases in the triplets encoding themo Initial amino acid incorporated into all proteins is a modified form of methionine (N-formylmethionine) in bacteria AUG only codon for methionineo Three codons serve as termination codons (UAG, UAA, and UGA)IV. 13.5 The Genetic Code Has Been Confirmed in Studies of Phage MS2o MS2 is bacteriophage with only three genes on a 3500 base RNA genome This sequencing confirmed genetic code Co linear These genes specify coat protein, an RNA-directed replicase, and a maturation proteinV. 13.6 The Genetic Code Is Nearly Universalo Mitochondrial DNA revealed some exceptions to the universal genetic codeo Table 13.5 (lists exceptions)VI. 13.7 Different Initiation Points Create Overlapping Geneso Some viruses, overlapping genes (open reading frame, ORF) have been identified where initiation at different AUG positions out of frame with one another leads to distinct polypeptides (Fig 13.8)VII. 13.8 Transcription Synthesizes RNA on a DNA Templateo RNA is synthesized on a DNA template by the process of transcriptiono The genetic information stored in DNA is transferred to RNA, which serves as the intermediate molecule between DNA and proteinsVIII. 13.9 Studies with Bacteria and Phages Provided Evidence for the Existence of mRNAo Analysis of RNA produced immediately after bacteriophage infection of E. coli shows that the base composition of the newly synthesized RNA resembles that of the phageDNA and not that of the bacterial host This suggests that RNA synthesis may be preliminary step in protein synthesis Use phage that doesn’t have same ATCG content as host Table 13.6IX. 13.10 RNA Polymerase Directs RNA Synthesiso RNA polymerase: directs the synthesis of RNA using a DNA template.  No primer required Enzyme uses ribonucleotides instead of dexoyribonucleotides Note reactiono RNA polymerase in E. coli contained  Alpha 2, Beta, Beta prime, omega, sigma (entire thing)o Transcription begins with template binding by RNA polymerase at a promoter (Fig. 13.9) Promoter: where you start, tend to have negative numbers Sigma subunit responsible for promoter recognition, leaves once done elongating and could start another section Transcription begins at transcription starting site, where DNA double helix is unwound to make template strand accessible to the action of RNA polymerase (called transcription start site=promoter site)o E. coli promoters have two consensus sequences: TTGACA and TATAAT (Pribnow box),positioned at -35 and -10 with respect to the transcription initiation site Mutation in any region often diminish transcription, sometimes severely  Numbers are rarely 100 % in consensus sequences, Once initiation has